Figure 5

dN/dS score visualization on the surface of gp120 (a close-up view of the interaction site between gp120 of patient F and the IgGb12 heavy chain (pdb code NY7)). Visualization of the dN/dS score (the posterior mean value derived from the Empirical Bayes approach using Model M8) onto the molecular surface of gp120 (pdb code 2B4C) using a color grade scale. Sites with no data or with a dN/dS score < 0.002 are depicted in white, sites with a dN/dS score between 0.002 and 0.15 are in light blue, sites between 0.15 and 1 are in light brown, sites with a dN/dS score between 1 and 2 are yellow, sites with a dN/dS score between 2 and 3 are orange, sites with a dN/dS score > 3 are red on the surface. Residues that are involved only in CD4 binding are depicted in blue, residues involved in IgGb12 binding are depicted in yellow, residues that interact both with CD4 and IgGb12 are displayed in green colour (modified from Zhou et al, 2007). The alpha helix present in the C3 region is shown in magenta. The carbon atoms of CDR1, CDR2 and CDR3 are coloured white, green and cyan respectively. The amino acid residues are shown as sticks. Of note, the binding region of the broadly neutralizing antibody overlaps the positively selected sites in the patient G derived structure.